Objective To determine the autopsy acceptance rate and reasons for decline at Mulago Hospital, Kampala, Uganda. Methods The next of kin of patients who died in a combined infectious diseases and gastro-enterology ward of Mulago Hospital were approached to answer a questionnaire concerning characteristics of their deceased relative. During the interview their consent was asked to perform a complete autopsy. If autopsy was declined, the next of kin were asked to provide their reason for the decline. Results Permission to perform an autopsy was requested in 158 (54%) of the 290 deaths that occurred during the study period. In 60 (38%) cases autopsy was accepted. Fifty-nine autopsies were performed. For 82% of refusals a reason was listed; mainly not wanting to delay the burial (58%), no use to know the cause of death (16%) and being satisfied with the clinical cause of death (10%). Conclusion The autopsy rate achieved under study conditions was 38% compared to rates of 5% in Mulago Hospital over the past decade. Timely request and rapid performance of autopsies appear to be important determinants of autopsy acceptance. A motivated team of pathologists and clinicians is required to increase autopsy acceptance.